Variant chr6-116732074-TTATATA-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_001366306.2(KPNA5):c.1433-19_1433-14delTATATA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00447 in 67,626 control chromosomes in the GnomAD database, including 1 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. There are indicators that this mutation may affect the branch point..

Frequency

Genomes: 𝑓 0.0058 ( 1 hom., cov: 0)

Exomes 𝑓: 0.0015 ( 0 hom. )

Consequence

KPNA5
NM_001366306.2 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.00

Variant links:

Genes affected

KPNA5 (HGNC:6398): (karyopherin subunit alpha 5) The transport of molecules between the nucleus and the cytoplasm in eukaryotic cells is mediated by the nuclear pore complex (NPC) which consists of 60-100 proteins and is probably 120 million daltons in molecular size. Small molecules (up to 70 kD) can pass through the nuclear pore by nonselective diffusion; larger molecules are transported by an active process. Most nuclear proteins contain short basic amino acid sequences known as nuclear localization signals (NLSs). KPNA5 protein belongs to the importin alpha protein family and is thought to be involved in NLS-dependent protein import into the nucleus. [provided by RefSeq, Jul 2008]

KPNA5 links:

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KPNA5	NM_001366306.2 linkuse as main transcript	c.1433-19_1433-14delTATATA		intron_variant		ENST00000368564.7	NP_001353235.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KPNA5	ENST00000368564.7 linkuse as main transcript	c.1433-19_1433-14delTATATA		intron_variant		1	NM_001366306.2	ENSP00000357552.1		O15131

Frequencies

GnomAD3 genomes

AF:

0.00579

AC:

271

AN:

46820

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00372

Gnomad AMI

AF:

0.00714

Gnomad AMR

AF:

0.00494

Gnomad ASJ

AF:

0.00211

Gnomad EAS

AF:

0.00415

Gnomad SAS

AF:

0.00552

Gnomad FIN

AF:

0.0478

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00581

Gnomad OTH

AF:

0.00321

GnomAD4 exome

AF:

0.00149

AC:

AN:

20806

Hom.:

AF XY:

0.00178

AC XY:

AN XY:

11802

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.00139

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.000952

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.00503

Gnomad4 NFE exome

AF:

0.00101

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

AF:

0.00579

AC:

271

AN:

46820

Hom.:

Cov.:

AF XY:

0.00600

AC XY:

129

AN XY:

21496

show subpopulations

Gnomad4 AFR

AF:

0.00372

Gnomad4 AMR

AF:

0.00494

Gnomad4 ASJ

AF:

0.00211

Gnomad4 EAS

AF:

0.00420

Gnomad4 SAS

AF:

0.00552

Gnomad4 FIN

AF:

0.0478

Gnomad4 NFE

AF:

0.00581

Gnomad4 OTH

AF:

0.00319

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BranchPoint Hunter

2.0

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over